[OpenSPIM] Multiview deconvolution - output image scaling

[Stephan.Preibisch at mdc-berlin.de]

Hi, no, this is only faster for finding the beads but does not influence the scaling. Only if you explicitly concatenate a transformation that does so (Right Click > Apply Transformation).

Feel free to ask more if it is unclear ...

All the best,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute of Medical Systems Biology of the MDC
Building 89, 1.08b

email: stephan.preibisch at mdc-berlin.de<mailto:stephan.preibisch at mdc-berlin.de>
web: http://www.preibisch.net/<http://fly.mpi-cbg.de/preibisch>

On 05 Aug 2016, at 15:08, Anthony, Neil <nantho2 at emory.edu<mailto:nantho2 at emory.edu>> wrote:

Thank you Stephan for your speedy response.

I do downsample x4 in xy when defining the beads…  Does this downsampling continue through to the alignment and MV decon too?  If so, would the output image be  2.56 um instead?

Assuming the above, should I only use downsampling when I’m checking that the alignment will work, but then start fresh without downsampling to attain the full resolution?

Thanks again for your time.
Neil

From: Stephan.Preibisch at mdc-berlin.de<mailto:Stephan.Preibisch at mdc-berlin.de> [mailto:Stephan.Preibisch at mdc-berlin.de]
Sent: Friday, August 05, 2016 4:47 AM
To: openspim at openspim.org<mailto:openspim at openspim.org>
Cc: Pavel Tomancak <tomancak at mpi-cbg.de>; Anthony, Neil <nantho2 at emory.edu>
Subject: Re: [OpenSPIM] Multiview deconvolution - output image scaling

Hi, by default the resolution of the output image is equal to the highest resolved dimension, so in your case 0.64x0.64x0.64 um. If you, however, manually apply any scaling during the alignment process it can be different.

All the best,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute of Medical Systems Biology of the MDC
Building 89, 1.08b

email: stephan.preibisch at mdc-berlin.de<mailto:stephan.preibisch at mdc-berlin.de>
web: http://www.preibisch.net/<http://fly.mpi-cbg.de/preibisch>

On 05 Aug 2016, at 08:55, Pavel Tomancak <tomancak at mpi-cbg.de<mailto:tomancak at mpi-cbg.de>> wrote:

FYI


From: "Anthony, Neil" <nantho2 at emory.edu<mailto:nantho2 at emory.edu>>

Subject: [OpenSPIM] Multiview deconvolution - output image scaling

Date: August 4, 2016 5:06:15 PM GMT+02:00

To: "openspim at openspim.org<mailto:openspim at openspim.org>" <openspim at openspim.org<mailto:openspim at openspim.org>>


Hi guys, I hope the scope are treating you well.

I was wondering what the output image scaling is after the Multiview deconvolution.  I provide the input image scaling of 0.64 x 0.64 x 3 um, and I’m assuming after the different angles have been factored in the output would have a more isotropic scaling…?

Does anybody know where to find that information?

Thanks
Neil


________________________________

This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
_______________________________________________
OpenSPIM mailing list
OpenSPIM at openspim.org<mailto:OpenSPIM at openspim.org>
http://openspim.org/mailman/listinfo/openspim

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://openspim.org/pipermail/openspim/attachments/20160805/bc81a035/attachment-0001.html>